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Acharya K, Shaw S, Bhattacharya SP, Biswas S, Bhandary S, Bhattacharya A. Pigments from pathogenic bacteria: a comprehensive update on recent advances. World J Microbiol Biotechnol 2024; 40:270. [PMID: 39030429 DOI: 10.1007/s11274-024-04076-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2024] [Accepted: 07/08/2024] [Indexed: 07/21/2024]
Abstract
Bacterial pigments stand out as exceptional natural bioactive compounds with versatile functionalities. The pigments represent molecules from distinct chemical categories including terpenes, terpenoids, carotenoids, pyridine, pyrrole, indole, and phenazines, which are synthesized by diverse groups of bacteria. Their spectrum of physiological activities encompasses bioactive potentials that often confer fitness advantages to facilitate the survival of bacteria amid challenging environmental conditions. A large proportion of such pigments are produced by bacterial pathogens mostly as secondary metabolites. Their multifaceted properties augment potential applications in biomedical, food, pharmaceutical, textile, paint industries, bioremediation, and in biosensor development. Apart from possessing a less detrimental impact on health with environmentally beneficial attributes, tractable and scalable production strategies render bacterial pigments a sustainable option for novel biotechnological exploration for untapped discoveries. The review offers a comprehensive account of physiological role of pigments from bacterial pathogens, production strategies, and potential applications in various biomedical and biotechnological fields. Alongside, the prospect of combining bacterial pigment research with cutting-edge approaches like nanotechnology has been discussed to highlight future endeavours.
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Affiliation(s)
- Kusumita Acharya
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | - Swarna Shaw
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | | | - Shatarupa Biswas
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India
| | - Suman Bhandary
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.
| | - Arijit Bhattacharya
- AMR-Research Laboratory, Department of Biological Sciences, Adamas University, Barasat-Barrackpore Rd, Kolkata, 700126, India.
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2
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Lu W, Shi R, Li X, Ma S, Yang D, Shang D, Xia Q. A review on complete silk gene sequencing and de novo assembly of artificial silk. Int J Biol Macromol 2024; 264:130444. [PMID: 38417762 DOI: 10.1016/j.ijbiomac.2024.130444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 02/22/2024] [Accepted: 02/23/2024] [Indexed: 03/01/2024]
Abstract
Silk, especially spider and insect silk, is a highly versatile biomaterial with potential applications in biomedicine, materials science, and biomimetic engineering. The primary structure of silk proteins is the basis for the mechanical properties of silk fibers. Biotechnologies such as single-molecule sequencing have facilitated an increasing number of reports on new silk genes and assembled silk proteins. Therefore, this review aims to provide a comprehensive overview of the recent advances in representative spider and insect silk proteins, focusing on identification methods, sequence characteristics, and de novo design and assembly. The review discusses three identification methods for silk genes: polymerase chain reaction (PCR)-based sequencing, PCR-free cloning and sequencing, and whole-genome sequencing. Moreover, it reveals the main spider and insect silk proteins and their sequences. Subsequent de novo assembly of artificial silk is covered and future research directions in the field of silk proteins, including new silk genes, customizable artificial silk, and the expansion of silk production and applications are discussed. This review provides a basis for the genetic aspects of silk production and the potential applications of artificial silk in material science and biomedical engineering.
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Affiliation(s)
- Wei Lu
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Run Shi
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Xue Li
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Sanyuan Ma
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Daiying Yang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Deli Shang
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China
| | - Qingyou Xia
- Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City, Biological Science Research Center, Southwest University, Chongqing, China.
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3
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Zhao M, Zhang XS, Xiong LB, Liu K, Li XF, Liu Y, Wang FQ. Establishment of an Efficient Expression and Regulation System in Streptomyces for Economical and High-Level Production of the Natural Blue Pigment Indigoidine. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:483-492. [PMID: 38146267 DOI: 10.1021/acs.jafc.3c05696] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
Indigoidine, as a kind of natural blue pigment, is widely used in textiles, food, and pharmaceuticals and is mainly synthesized from l-glutamine via a condensation reaction by indigoidine synthetases, most of which originates from Streptomyces species. However, due to the complex metabolic switches of Streptomyces, most of the researchers choose to overexpress indigoidine synthetases in the heterologous host to achieve high-level production of indigoidine. Considering the advantages of low-cost culture medium and simple culture conditions during the large-scale culture of Streptomyces, here, an updated regulation system derived from the Streptomyces self-sustaining system, constructed in our previous study, was established for the highly efficient production of indigoidine in Streptomyces lividans TK24. The updated system was constructed via promoter mining and σhrdB expression optimization, and this system was applied to precisely and continuously regulate the expression of indigoidine synthetase IndC derived from Streptomyces albus J1704. Finally, the engineered strain was cultured with cheap industrial glycerol as a supplementary carbon source, and 14.3 and 46.27 g/L indigoidine could be achieved in a flask and a 4 L fermentor, respectively, reaching the highest level of microbial synthesis of indigoidine. This study will lay a foundation for the industrial application of Streptomyces cell factories to produce indigoidine.
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Affiliation(s)
- Ming Zhao
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Xiu-Shan Zhang
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Liang-Bin Xiong
- Shanghai Key Laboratory of Molecular Imaging, School of Pharmacy, Shanghai University of Medicine and Health Sciences, Shanghai 201318, China
| | - Kun Liu
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Xiang-Fei Li
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Yan Liu
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biological and Food Engineering, Anhui Polytechnic University, Wuhu 241000, China
| | - Feng-Qing Wang
- State Key Laboratory of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai 200237, China
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Pasdaran A, Zare M, Hamedi A, Hamedi A. A Review of the Chemistry and Biological Activities of Natural Colorants, Dyes, and Pigments: Challenges, and Opportunities for Food, Cosmetics, and Pharmaceutical Application. Chem Biodivers 2023; 20:e202300561. [PMID: 37471105 DOI: 10.1002/cbdv.202300561] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Revised: 07/17/2023] [Accepted: 07/20/2023] [Indexed: 07/21/2023]
Abstract
Natural pigments are important sources for the screening of bioactive lead compounds. This article reviewed the chemistry and therapeutic potentials of over 570 colored molecules from plants, fungi, bacteria, insects, algae, and marine sources. Moreover, related biological activities, advanced extraction, and identification approaches were reviewed. A variety of biological activities, including cytotoxicity against cancer cells, antioxidant, anti-inflammatory, wound healing, anti-microbial, antiviral, and anti-protozoal activities, have been reported for different pigments. Considering their structural backbone, they were classified as naphthoquinones, carotenoids, flavonoids, xanthones, anthocyanins, benzotropolones, alkaloids, terpenoids, isoprenoids, and non-isoprenoids. Alkaloid pigments were mostly isolated from bacteria and marine sources, while flavonoids were mostly found in plants and mushrooms. Colored quinones and xanthones were mostly extracted from plants and fungi, while colored polyketides and terpenoids are often found in marine sources and fungi. Carotenoids are mostly distributed among bacteria, followed by fungi and plants. The pigments isolated from insects have different structures, but among them, carotenoids and quinone/xanthone are the most important. Considering good manufacturing practices, the current permitted natural colorants are: Carotenoids (canthaxanthin, β-carotene, β-apo-8'-carotenal, annatto, astaxanthin) and their sources, lycopene, anthocyanins, betanin, chlorophyllins, spirulina extract, carmine and cochineal extract, henna, riboflavin, pyrogallol, logwood extract, guaiazulene, turmeric, and soy leghemoglobin.
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Affiliation(s)
- Ardalan Pasdaran
- Department of Pharmacognosy, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Maryam Zare
- Department of Pharmacognosy, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Student research committee, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Azar Hamedi
- School of Agriculture, Shiraz University, Shiraz, Iran
| | - Azadeh Hamedi
- Department of Pharmacognosy, School of Pharmacy, Shiraz University of Medical Sciences, Shiraz, Iran
- Medicinal Plants Processing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
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Jia L, Lu W, Hu D, Feng M, Wang A, Wang R, Sun H, Wang P, Xia Q, Ma S. Genetically engineered Blue silkworm capable of synthesizing natural blue pigment. Int J Biol Macromol 2023; 235:123863. [PMID: 36870637 DOI: 10.1016/j.ijbiomac.2023.123863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/23/2023] [Accepted: 02/24/2023] [Indexed: 03/06/2023]
Abstract
Synthetic biology is an eco-friendly and sustainable approach for the production of compounds, particularly used when the production processes involve toxic reagents. In this study, we used the silk gland of silkworm to produce indigoidine, a valuable natural blue pigment that cannot be synthesized naturally in animals. We genetically engineered these silkworms by integrating the indigoidine synthetase (idgS) gene from S. lavendulae and the PPTase (Sfp) gene from B. subtilis into the silkworm genome. In the resulting Blue silkworm, indigoidine was detected at a high level in the posterior silk gland (PSG), spanning all developmental stages from larvae to adults, without affecting silkworm growth or development. This synthesized indigoidine was secreted from the silk gland and subsequently stored in the fat body, with only a small fraction being excreted by the Malpighian tubule. Metabolomic analysis revealed that Blue silkworm efficiently synthesized indigoidine by upregulating l-glutamine, the precursor of indigoidine, and succinate, which is related to energy metabolism in the PSG. This study represents the first synthesis of indigoidine in an animal and therefore opens a new avenue for the biosynthesis of natural blue pigments and other valuable small molecules.
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Affiliation(s)
- Ling Jia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China; Integrative Science Center of Gerplasm Greation in Western China (CHONGQING) Science City & Southwest University, Chongqing 400715, China
| | - Wei Lu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China; Integrative Science Center of Gerplasm Greation in Western China (CHONGQING) Science City & Southwest University, Chongqing 400715, China
| | - Dan Hu
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Min Feng
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China
| | - Aoming Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Ruolin Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Hao Sun
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Pan Wang
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China
| | - Qingyou Xia
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China; Integrative Science Center of Gerplasm Greation in Western China (CHONGQING) Science City & Southwest University, Chongqing 400715, China.
| | - Sanyuan Ma
- State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing 400715, China; Biological Science Research Center, Southwest University, Chongqing 400715, China; Integrative Science Center of Gerplasm Greation in Western China (CHONGQING) Science City & Southwest University, Chongqing 400715, China.
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6
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Abstract
Conventional dyeing processes currently practiced in the textile industry have a great environmental impact, mainly in relation to the quantity and pollution of water, use of toxic chemicals, atmospheric emissions, and high energy consumption. This study aims to discuss the relationship between the variables that involve conventional dyeing processes and environmental issues. It presents the mapping of the materials and emerging technologies for ecological coloration, specifically for the pretreatment and dyeing stages. Regarding pretreatment, it discusses biochemical (enzymes) and physical treatment (ultraviolet radiation, plasma, and ozone technology) approaches. With respect to the dyeing processes, it addresses ecological materials (natural dyes) and emerging technologies (such as plasma, supercritical CO2, AirDye®, ultrasonic, microwave, Nano-DyeTM, and electrochemical). Given the importance of ecological coloration, this study provides important reflections on the urgency of resolving issues related to barriers and economic viability in the implementation of the alternatives presented and demonstrates the need to develop educational projects to prepare fashion and textile professionals.
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7
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Panchanawaporn S, Chutrakul C, Jeennor S, Anantayanon J, Rattanaphan N, Laoteng K. Potential of Aspergillus oryzae as a biosynthetic platform for indigoidine, a non-ribosomal peptide pigment with antioxidant activity. PLoS One 2022; 17:e0270359. [PMID: 35737654 PMCID: PMC9223385 DOI: 10.1371/journal.pone.0270359] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2022] [Accepted: 06/08/2022] [Indexed: 11/18/2022] Open
Abstract
The growing demand for natural pigments in the industrial sector is a significant driving force in the development of production processes. The production of natural blue pigments, which have wide industrial applications, using microbial systems has been gaining significant attention. In this study, we used Aspergillus oryzae as a platform cell factory to produce the blue pigment indigoidine (InK), by genetic manipulation of its non-ribosomal peptide synthetase system to overexpress the indigoidine synthetase gene (AoinK). Phenotypic analysis showed that InK production from the engineered strain was growth associated, owing to the constitutive control of gene expression. Furthermore, the initial pH, temperature, and glutamine and MgSO4 concentrations were key factors affecting InK production by the engineered strain. The pigment secretion was enhanced by addition of 1% Tween 80 solution to the culture medium. The maximum titer of total InK was 1409.22 ± 95.33 mg/L, and the maximum productivity was 265.09 ± 14.74 mg/L·d. Moreover, the recombinant InK produced by the engineered strain exhibited antioxidant activity. These results indicate that A. oryzae has the potential to be used as a fungal platform for overproduction of extracellular non-ribosomal peptide pigments.
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Affiliation(s)
- Sarocha Panchanawaporn
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Chanikul Chutrakul
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
- * E-mail:
| | - Sukanya Jeennor
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Jutamas Anantayanon
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Nakul Rattanaphan
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
| | - Kobkul Laoteng
- Functional Ingredients and Food Innovation Research Group (IFIG), National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Khlong Luang, Pathum Thani, Thailand
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Iwai K, Wehrs M, Garber M, Sustarich J, Washburn L, Costello Z, Kim PW, Ando D, Gaillard WR, Hillson NJ, Adams PD, Mukhopadhyay A, Garcia Martin H, Singh AK. Scalable and automated CRISPR-based strain engineering using droplet microfluidics. MICROSYSTEMS & NANOENGINEERING 2022; 8:31. [PMID: 35359611 PMCID: PMC8924257 DOI: 10.1038/s41378-022-00357-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 09/21/2021] [Accepted: 10/18/2021] [Indexed: 06/14/2023]
Abstract
We present a droplet-based microfluidic system that enables CRISPR-based gene editing and high-throughput screening on a chip. The microfluidic device contains a 10 × 10 element array, and each element contains sets of electrodes for two electric field-actuated operations: electrowetting for merging droplets to mix reagents and electroporation for transformation. This device can perform up to 100 genetic modification reactions in parallel, providing a scalable platform for generating the large number of engineered strains required for the combinatorial optimization of genetic pathways and predictable bioengineering. We demonstrate the system's capabilities through the CRISPR-based engineering of two test cases: (1) disruption of the function of the enzyme galactokinase (galK) in E. coli and (2) targeted engineering of the glutamine synthetase gene (glnA) and the blue-pigment synthetase gene (bpsA) to improve indigoidine production in E. coli.
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Affiliation(s)
- Kosuke Iwai
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Maren Wehrs
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Megan Garber
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Jess Sustarich
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Lauren Washburn
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Zachary Costello
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Peter W. Kim
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - David Ando
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - William R. Gaillard
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
| | - Nathan J. Hillson
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Paul D. Adams
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- Department of Bioengineering, University of California, Berkeley, CA 94720 USA
| | - Aindrila Mukhopadhyay
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
| | - Hector Garcia Martin
- Biofuels and Bioproducts Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720 USA
- BCAM, Basque Center for Applied Mathematics, Bilbao, 48009 Spain
| | - Anup K. Singh
- Technology Division, DOE Joint BioEnergy Institute, Emeryville, CA 94608 USA
- Biotechnology and Bioengineering Department, Sandia National Laboratories, Livermore, CA 94550 USA
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Fortinez CM, Bloudoff K, Harrigan C, Sharon I, Strauss M, Schmeing TM. Structures and function of a tailoring oxidase in complex with a nonribosomal peptide synthetase module. Nat Commun 2022; 13:548. [PMID: 35087027 PMCID: PMC8795117 DOI: 10.1038/s41467-022-28221-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 12/19/2021] [Indexed: 12/15/2022] Open
Abstract
Nonribosomal peptide synthetases (NRPSs) are large modular enzymes that synthesize secondary metabolites and natural product therapeutics. Most NRPS biosynthetic pathways include an NRPS and additional proteins that introduce chemical modifications before, during or after assembly-line synthesis. The bacillamide biosynthetic pathway is a common, three-protein system, with a decarboxylase that prepares an NRPS substrate, an NRPS, and an oxidase. Here, the pathway is reconstituted in vitro. The oxidase is shown to perform dehydrogenation of the thiazoline in the peptide intermediate while it is covalently attached to the NRPS, as the penultimate step in bacillamide D synthesis. Structural analysis of the oxidase reveals a dimeric, two-lobed architecture with a remnant RiPP recognition element and a dramatic wrapping loop. The oxidase forms a stable complex with the NRPS and dimerizes it. We visualized co-complexes of the oxidase bound to the elongation module of the NRPS using X-ray crystallography and cryo-EM. The three active sites (for adenylation, condensation/cyclization, and oxidation) form an elegant arc to facilitate substrate delivery. The structures enabled a proof-of-principle bioengineering experiment in which the BmdC oxidase domain is embedded into the NRPS.
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Affiliation(s)
- Camille Marie Fortinez
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Kristjan Bloudoff
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Connor Harrigan
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Itai Sharon
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada.,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada
| | - Mike Strauss
- Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.,Department of Anatomy and Cell Biology, McGill University, Montréal, QC, H3A 0C7, Canada
| | - T Martin Schmeing
- Department of Biochemistry, McGill University, Montréal, QC, H3G 0B1, Canada. .,Centre de recherche en biologie structurale, McGill University, Montréal, QC, H3G 0B1, Canada.
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10
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Seo SO, Jin YS. Next-Generation Genetic and Fermentation Technologies for Safe and Sustainable Production of Food Ingredients: Colors and Flavorings. Annu Rev Food Sci Technol 2022; 13:463-488. [DOI: 10.1146/annurev-food-052720-012228] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A growing human population is a significant issue in food security owing to the limited land and resources available for agricultural food production. To solve these problems, sustainable food manufacturing processes and the development of alternative foods and ingredients are needed. Metabolic engineering and synthetic biology can help solve the food security issue and satisfy the demand for alternative food production. Bioproduction of food ingredients by microbial fermentation is a promising method to replace current manufacturing processes, such as extraction from natural materials and chemical synthesis, with more ecofriendly and sustainable operations. This review highlights successful examples of bioproduction for food additives by engineered microorganisms, with an emphasis on colorants and flavors that are extensively used in the food industry. Recent strain engineering developments and fermentation strategies for producing selected food colorants and flavors are introduced with discussions on the current status and future perspectives. Expected final online publication date for the Annual Review of Food Science and Technology, Volume 13 is March 2022. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.
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Affiliation(s)
- Seung-Oh Seo
- Department of Food Science and Nutrition, Catholic University of Korea, Bucheon, Republic of Korea
| | - Yong-Su Jin
- Department of Food Science and Human Nutrition and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
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11
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Ren J, Tang W, Barton CD, Price OM, Mortensen MW, Phillips A, Wald B, Hulme SE, Stanley LP, Hevel J, Zhan J. A highly versatile fungal glucosyltransferase for specific production of quercetin-7-O-β-D-glucoside and quercetin-3-O-β-D-glucoside in different hosts. Appl Microbiol Biotechnol 2021; 106:227-245. [PMID: 34874472 DOI: 10.1007/s00253-021-11716-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 12/22/2022]
Abstract
Glycosylation is an effective way to improve the water solubility of natural products. In this work, a novel glycosyltransferase gene (BbGT) was discovered from Beauveria bassiana ATCC 7159 and heterologously expressed in Escherichia coli. The purified enzyme was functionally characterized through in vitro enzymatic reactions as a UDP-glucosyltransferase, converting quercetin to five monoglucosylated and one diglucosylated products. The optimal pH and temperature for BbGT are 35 ℃ and 8.0, respectively. The activity of BbGT was stimulated by Ca2+, Mg2+, and Mn2+, but inhibited by Zn2+. BbGT enzyme is flexible and can glycosylate a variety of substrates such as curcumin, resveratrol, and zearalenone. The enzyme was also expressed in other microbial hosts including Saccharomyces cerevisiae, Pseudomonas putida, and Pichia pastoris. Interestingly, the major glycosylation product of quercetin in E. coli, P. putida, and P. pastoris was quercetin-7-O-β-D-glucoside, while the enzyme dominantly produced quercetin-3-O-β-D-glucoside in S. cerevisiae. The BbGT-harboring E. coli and S. cerevisiae strains were used as whole-cell biocatalysts to specifically produce the two valuable quercetin glucosides, respectively. The titer of quercetin-7-O-β-D-glucosides was 0.34 ± 0.02 mM from 0.83 mM quercetin in 24 h by BbGT-harboring E. coli. The yield of quercetin-3-O-β-D-glucoside was 0.22 ± 0.02 mM from 0.41 mM quercetin in 12 h by BbGT-harboring S. cerevisiae. This work thus provides an efficient way to produce two valuable quercetin glucosides through the expression of a versatile glucosyltransferase in different hosts. KEY POINTS: • A highly versatile glucosyltransferase was identified from B. bassiana ATCC 7159. • BbGT converts quercetin to five mono- and one di-glucosylated derivatives in vitro. • Different quercetin glucosides were produced by BbGT in E. coli and S. cerevisiae.
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Affiliation(s)
- Jie Ren
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Wenzhu Tang
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA.,School of Biological Engineering, Dalian Polytechnic University, Dalian, 116034, Liaoning, China
| | - Caleb Don Barton
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Owen M Price
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322-0300, USA
| | - Mark Wayne Mortensen
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Alexandra Phillips
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Banner Wald
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Simon Elgin Hulme
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Logan Powell Stanley
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA
| | - Joan Hevel
- Department of Chemistry and Biochemistry, Utah State University, 0300 Old Main Hill, Logan, UT, 84322-0300, USA
| | - Jixun Zhan
- Department of Biological Engineering, Utah State University, 4105 Old Main Hill, Logan, UT, 84322-4105, USA.
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12
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Hui CY, Guo Y, Li LM, Liu L, Chen YT, Yi J, Zhang NX. Indigoidine biosynthesis triggered by the heavy metal-responsive transcription regulator: a visual whole-cell biosensor. Appl Microbiol Biotechnol 2021; 105:6087-6102. [PMID: 34291315 DOI: 10.1007/s00253-021-11441-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 06/22/2021] [Accepted: 07/03/2021] [Indexed: 10/20/2022]
Abstract
During the last few decades, whole-cell biosensors have attracted increasing attention for their enormous potential in monitoring bioavailable heavy metal contaminations in the ecosystem. Visual and measurable output signals by employing natural pigments have been demonstrated to offer another potential choice to indicate the existence of bioavailable heavy metals in recent years. The biosynthesis of the blue pigment indigoidine has been achieved in E. coli following heterologous expression of both BpsA (a single-module non-ribosomal peptide synthetase) and PcpS (a PPTase to activate apo-BpsA). Moreover, we demonstrated herein the development of the indigoidine-based whole-cell biosensors to detect bioavailable Hg(II) and Pb(II) in water samples by employing metal-responsive transcriptional regulator MerR and PbrR as the sensory elements, and the indigoidine biosynthesis gene cluster as a reporter element. The resulting indigoidine-based biosensors presented a good selectivity and high sensitivity to target metal ions. High concentration of target metal exposure could be clearly recognized by the naked eye due to the color change by the secretion of indigoidine, and quantified by measuring the absorbance of the culture supernatants at 600 nm. Dose-response relationships existed between the exposure concentrations of target heavy metals and the production of indigoidine. Although fairly good linear relationships were obtained in a relatively limited concentration range of the concentrations of heavy metal ions, these findings suggest that genetically controlled indigoidine biosynthesis triggered by the MerR family transcriptional regulator can enable a sensitive, visual, and qualitative whole-cell biosensor for bioindicating the presence of bioaccessible heavy metal in environmental water samples. KEY POINTS: • Biosynthesis pathway of indigoidine reconstructed in a high copy number plasmid in E. coli. • Visual and colorimetric detection of Hg(II) and Pb(II) by manipulation of indigoidine biosynthesis through MerR family metalloregulator. •Enhanced detection sensitivity toward Hg(II) and Pb(II) achieved using novel pigment-based whole-cell biosensors.
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Affiliation(s)
- Chang-Ye Hui
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
| | - Yan Guo
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Li-Mei Li
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Lisa Liu
- Lewis Katz School of Medicine, Temple University, Philadelphia, PA, USA
| | - Yu-Ting Chen
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Juan Yi
- Department of Pathology & Toxicology, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China
| | - Nai-Xing Zhang
- National Key Clinical Specialty of Occupational Diseases, Shenzhen Prevention and Treatment Center for Occupational Diseases, Shenzhen, China.
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13
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Engineering Heterologous Hosts for the Enhanced Production of Non-ribosomal Peptides. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0080-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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14
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Draft Genome Sequence of a Highly Pigmented Bacterium Paracoccus marcusii KGP Capable of Producing Galacto-oligosaccharides Synthesising Enzyme. Curr Microbiol 2021; 78:634-641. [PMID: 33394084 DOI: 10.1007/s00284-020-02326-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2020] [Accepted: 12/09/2020] [Indexed: 12/31/2022]
Abstract
The genome of Paracoccus marcusii KGP, isolated from the marine sediment collected from the coast of the Bay of Bengal, was sequenced using Oxford Nanopore sequencing technology. The assembled genome sequence consists of seven contigs and has a 4,085,678 bp circular chromosome with 1647 coding genes and a G+C content of 66.7%. Besides, the genome of P. marcusii KGP contains three copies of the rrn operon. The genes coding for the industrially relevant enzymes and secondary metabolites such as β-galactosidase, protease, amylase, β-glucosidase, ectoine, indigoidine, and carotenoid biosynthesis clusters were also identified in the genome. When the β-galactosidase extracted from P. marcusii KGP was mixed with a high concentration of lactose, galacto-oligosaccharides were produced, which revealed the transgalactosylation property of the enzyme. The genome sequence of P. marcusii KGP was found to have an average nucleotide identity value of 96.16 and a digital DNA-DNA hybridisation value of 73.90% with the genome sequence of P. marcusii CGMCC. Furthermore, by comparing the genome sequences of both strains, it was found that the size of the KGP genome was large, indicating the possibility of strain-specific genes in addition to core genes.
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15
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Sun L, Xin F, Alper HS. Bio-synthesis of food additives and colorants-a growing trend in future food. Biotechnol Adv 2021; 47:107694. [PMID: 33388370 DOI: 10.1016/j.biotechadv.2020.107694] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Revised: 12/24/2020] [Accepted: 12/27/2020] [Indexed: 02/07/2023]
Abstract
Food additives and colorants are extensively used in the food industry to improve food quality and safety during processing, storage and packing. Sourcing of these molecules is predominately through three means: extraction from natural sources, chemical synthesis, and bio-production, with the first two being the most utilized. However, growing demands for sustainability, safety and "natural" products have renewed interest in using bio-based production methods. Likewise, the move to more cultured foods and meat alternatives requires the production of new additives and colorants. The production of bio-based food additives and colorants is an interdisciplinary research endeavor and represents a growing trend in future food. To highlight the potential of microbial hosts for food additive and colorant production, we focus on current advances for example molecules based on their utilization stage and bio-production yield as follows: (I) approved and industrially produced with high titers; (II) approved and produced with decent titers (in the g/L range), but requiring further engineering to reduce production costs; (III) approved and produced with very early stage titers (in the mg/L range); and (IV) new/potential candidates that have not been approved but can be sourced through microbes. Promising approaches, as well as current challenges and future directions will also be thoroughly discussed for the bioproduction of these food additives and colorants.
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Affiliation(s)
- Lichao Sun
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Fengjiao Xin
- Institute of Food Science and Technology, Chinese Academy of Agricultural Sciences, Beijing 100193, People's Republic of China.
| | - Hal S Alper
- Institute for Cellular and Molecular Biology, The University of Texas at Austin, 2500 Speedway Avenue, Austin, TX 78712, United States; McKetta Department of Chemical Engineering, The University of Texas at Austin, 200 E Dean Keeton St. Stop C0400, Austin, TX 78712, United States.
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16
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Sakai-Kawada FE, Ip CG, Hagiwara KA, Nguyen HYX, Yakym CJAV, Helmkampf M, Armstrong EE, Awaya JD. Characterization of Prodiginine Pathway in Marine Sponge-Associated Pseudoalteromonas sp. PPB1 in Hilo, Hawai‘i. FRONTIERS IN SUSTAINABLE FOOD SYSTEMS 2020. [DOI: 10.3389/fsufs.2020.600201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Interest in bioactive pigments stems from their ecological role in adaptation, as well as their applications in various consumer products. The production of these bioactive pigments can be from a variety of biological sources, including simple microorganisms that may or may not be associated with a host. This study is particularly interested in the marine sponges, which have been known to harbor microorganisms that produce secondary metabolites like bioactive pigments. In this study, marine sponge tissue samples were collected from Puhi Bay off the Eastern shore of Hilo, Hawai‘i and subsequently were identified as Petrosia sp. with red pigmentation. Using surface sterilization and aseptic plating of sponge tissue samples, sponge-associated microorganisms were isolated. One isolate (PPB1) produced a colony with red pigmentation like that of Petrosia sp., suggesting an integral relationship between this particular isolate and the sponge of interest. 16S characterization and sequencing of PPB1 revealed that it belonged to the Pseudoalteromonas genus. Using various biological assays, both antimicrobial and antioxidant bioactivity was shown in Pseudoalteromonas sp. PPB1 crude extract. To further investigate the genetics of pigment production, a draft genome of PPB1 was sequenced, assembled, and annotated. This revealed a prodiginine biosynthetic pathway and the first cited-incidence of a prodiginine-producing Pseudoalteromonas species isolated from a marine sponge host. Further understanding into the bioactivity and biosynthesis of secondary metabolites like pigmented prodiginine may uncover the complex ecological interactions between host sponge and microorganism.
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17
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Santos MCD, Bicas JL. Natural blue pigments and bikaverin. Microbiol Res 2020; 244:126653. [PMID: 33302226 DOI: 10.1016/j.micres.2020.126653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/26/2020] [Accepted: 11/13/2020] [Indexed: 10/22/2022]
Abstract
In last years, the main studied microbial sources of natural blue pigments have been the eukaryotic algae, Rhodophytes and Cryptophytes, and the cyanobacterium Arthrospira (Spirulina) platensis, responsible for the production of phycocyanin, one of the most important blue compounds approved for food and cosmetic use. Recent research also includes the indigoidine pigment from the bacteria Erwinia, Streptomyces and Photorhabdus. Despite these advances, there are still few options of microbial blue pigments reported so far, but the interest in these products is high due to the lack of stable natural blue pigments in nature. Filamentous fungi are particularly attractive for their ability to produce pigments with a wide range of colors. Bikaverin is a red metabolite present mainly in species of the genus Fusarium. Although originally red, the biomass containing bikaverin changes its color to blue after heat treatment, through a mechanism still unknown. In addition to the special behavior of color change by thermal treatment, bikaverin has beneficial biological properties, such as antimicrobial and antiproliferative activities, which can expand its use for the pharmaceutical and medical sectors. The present review addresses the production natural blue pigments and focuses on the properties of bikaverin, which can be an important source of blue pigment with potential applications in the food industry and in other industrial sectors.
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18
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Wang L, Sun Y, Lv D, Liu B, Guan Y, Yu D. Protein scaffold optimizes arrangement of constituent enzymes in indigoidine synthetic pathway to improve the pigment production. Appl Microbiol Biotechnol 2020; 104:10493-10502. [PMID: 33151367 DOI: 10.1007/s00253-020-10990-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 09/30/2020] [Accepted: 10/31/2020] [Indexed: 11/26/2022]
Abstract
Indigoidine is a dark-blue natural pigment with application prospect and synthesized from glutamine (Gln) by series of indigoidine synthetases (IndCs). Indigoidine production can be improved by enhancing Gln pool via supplementing Gln directly or converting metabolism glutamate (Glu) to Gln by glutamine synthetase (GlnA). But, Gln is expensive, and excess Gln inhibits indigoidine production of the recombinant strain. Supplementing Glu instead of Gln may improve the productive and economic efficiency of indigoidine, but the local activities and positions of the indigoidine pathway enzymes GlnA, Sc-IndC, and the helper protein of Sc-IndC (IndB) should be well arranged. We identified the Streptomyces chromofuscus ATCC 49982 derived IndC (Sc-IndC) as an more efficient IndC compared to other IndCs applied for constructing indigoidine-producting strains, and designed series of protein scaffold complexes with architectures of PDZ, SH3, and GBD domains (PxSyG1) to arrange the pathway enzymes. The strain recruiting GlnA, Sc-IndC, and IndB on the PDZ, SH3, and GBD domains of scaffold P1S2G1, respectively, was the most efficient. In the strain, the GlnA supplied sufficient local Gln for Sc-IndC from Glu, and the generated Gln was immediately consumed by Sc-IndC to relieve cell growth inhibition caused by Gln. The optimum Glu concentration (6 g/L) for the strain was higher than those of the strains recruiting Sc-IndC on the GBD domain, which was away from the PDZ domain recruiting GlnA. The highest titer of indigoidine was 12 g/L, which was two folds of the control without scaffold (5.8 g/L). The titer is 5 g/L higher than the control without Glu supplemented (6.9 g/L), meaning that 97% of the supplemented Glu was transformed into indigoidine. The batch fermentation with the optimum strain in a 5-L reactor achieved an indigoidine titer of 14 g/L in 60 h. To our knowledge, this was the most efficient indigoidine productivity achieved so far. The optimization strategies by protein scaffold should be applicative to other pathways with complex substrate demands. KEY POINTS: •Protein scaffold systems were designed to arrange the indigoidine synthetic pathway. •The scaffold system improved supplement of Gln for indigoidine production from Glu. •The inhibition caused by excess Gln was relieved by proper designed scaffold. •The yield and titer of indigoidine was improved by arranging the pathway enzymes. Graphical abstract.
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Affiliation(s)
- Lei Wang
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Yue Sun
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
- Viablife Biotech Co., Ltd, Hangzhou, 311113, China
| | - Di Lv
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Bin Liu
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Yuekai Guan
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China
| | - Dayu Yu
- Sci-Tech Center for Clean Conversion and High-valued Utilization of Biomass, Jilin Province, Northeast Electric Power University, Jilin, 132012, China.
- School of Chemical Engineering, Northeast Electric Power University, Jilin, 132012, China.
- Viablife Biotech Co., Ltd, Hangzhou, 311113, China.
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19
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Marques F, Luzhetskyy A, Mendes MV. Engineering Corynebacterium glutamicum with a comprehensive genomic library and phage-based vectors. Metab Eng 2020; 62:221-234. [DOI: 10.1016/j.ymben.2020.08.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 07/17/2020] [Accepted: 08/10/2020] [Indexed: 12/18/2022]
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20
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Banerjee D, Eng T, Lau AK, Sasaki Y, Wang B, Chen Y, Prahl JP, Singan VR, Herbert RA, Liu Y, Tanjore D, Petzold CJ, Keasling JD, Mukhopadhyay A. Genome-scale metabolic rewiring improves titers rates and yields of the non-native product indigoidine at scale. Nat Commun 2020; 11:5385. [PMID: 33097726 PMCID: PMC7584609 DOI: 10.1038/s41467-020-19171-4] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 09/30/2020] [Indexed: 01/06/2023] Open
Abstract
High titer, rate, yield (TRY), and scalability are challenging metrics to achieve due to trade-offs between carbon use for growth and production. To achieve these metrics, we take the minimal cut set (MCS) approach that predicts metabolic reactions for elimination to couple metabolite production strongly with growth. We compute MCS solution-sets for a non-native product indigoidine, a sustainable pigment, in Pseudomonas putida KT2440, an emerging industrial microbe. From the 63 solution-sets, our omics guided process identifies one experimentally feasible solution requiring 14 simultaneous reaction interventions. We implement a total of 14 genes knockdowns using multiplex-CRISPRi. MCS-based solution shifts production from stationary to exponential phase. We achieve 25.6 g/L, 0.22 g/l/h, and ~50% maximum theoretical yield (0.33 g indigoidine/g glucose). These phenotypes are maintained from batch to fed-batch mode, and across scales (100-ml shake flasks, 250-ml ambr®, and 2-L bioreactors).
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Affiliation(s)
- Deepanwita Banerjee
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Thomas Eng
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Andrew K Lau
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yusuke Sasaki
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Brenda Wang
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yan Chen
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jan-Philip Prahl
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Vasanth R Singan
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Robin A Herbert
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Yuzhong Liu
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Deepti Tanjore
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- Advanced Biofuel and Bioproduct Process Development Unit, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
| | - Christopher J Petzold
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Jay D Keasling
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
- QB3 Institute, University of California-Berkeley, 5885 Hollis Street, 4th Floor, Emeryville, CA, 94608, USA
- Department of Chemical & Biomolecular Engineering, University of California, Berkeley, CA, 94720, USA
- Department of Bioengineering, University of California, Berkeley, CA, 94720, USA
- Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, 2970, Horsholm, Denmark
- Synthetic Biochemistry Center, Institute for Synthetic Biology, Shenzhen Institutes for Advanced Technologies, Shenzhen, China
| | - Aindrila Mukhopadhyay
- Joint BioEnergy Institute, Lawrence Berkeley National Laboratory, Emeryville, CA, 94608, USA.
- Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA.
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21
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Pang B, Chen Y, Gan F, Yan C, Jin L, Gin JW, Petzold CJ, Keasling JD. Investigation of Indigoidine Synthetase Reveals a Conserved Active-Site Base Residue of Nonribosomal Peptide Synthetase Oxidases. J Am Chem Soc 2020; 142:10931-10935. [PMID: 32510939 DOI: 10.1021/jacs.0c04328] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Nonribosomal peptide synthetase (NRPS) oxidase (Ox) domains oxidize protein-bound intermediates to install crucial structural motifs in bioactive natural products. The mechanism of this domain remains elusive. Here, by studying indigoidine synthetase, a single-module NRPS involved in the biosynthesis of indigoidine and several other bacterial secondary metabolites, we demonstrate that its Ox domain utilizes an active-site base residue, tyrosine 665, to deprotonate a protein-bound l-glutaminyl residue. We further validate the generality of this active-site residue among NRPS Ox domains. These findings not only resolve the biosynthetic pathway mediated by indigoidine synthetase but enable mechanistic insight into NRPS Ox domains.
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Affiliation(s)
- Bo Pang
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Yan Chen
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Fei Gan
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Chunsheng Yan
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Liyuan Jin
- Joint BioEnergy Institute, Emeryville, California 94608, United States
| | - Jennifer W Gin
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Christopher J Petzold
- Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jay D Keasling
- QB3 Institute, University of California, Berkeley, Berkeley, California 94720, United States.,Joint BioEnergy Institute, Emeryville, California 94608, United States.,Biological Systems and Engineering Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Department of Chemical & Biomolecular Engineering and Department of Bioengineering, University of California, Berkeley, Berkeley, California 94720, United States.,Novo Nordisk Foundation Center for Biosustainability, Technical University Denmark, DK 2970 Horsholm, Denmark.,Center for Synthetic Biochemistry, Shenzhen Institutes for Advanced Technologies, Shenzhen 518055, P. R. China
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22
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Finger S, Godoy FA, Wittwer G, Aranda CP, Calderón R, Miranda CD. Purification and characterization of indochrome type blue pigment produced by Pseudarthrobacter sp. 34LCH1 isolated from Atacama desert. J Ind Microbiol Biotechnol 2018; 46:101-111. [PMID: 30377866 DOI: 10.1007/s10295-018-2088-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Accepted: 10/15/2018] [Indexed: 01/29/2023]
Abstract
The interest in and demand for natural dyes has increased significantly in recent years; however, very few natural blue dyes are commercially available, because blue colored compounds in nature are relatively rare. In this study, a blue pigment-producing bacteria from Lake Chungará (Atacama Desert, Chile) was isolated, and its blue pigment was purified and chemically characterized. The pigment-producing strain was identified as Pseudarthrobacter sp. by 16S rRNA gene sequencing. The pigment was separated from the filtered culture medium by column chromatography/solid-phase extraction using different resins (ionic exchange, C-18, size exclusion). The strain produced up to 2.5 g L-1 of blue pigment, which was very soluble in water, partially soluble in methanol and insoluble in other organic solvents. The pigment was analyzed and characterized by analytical HPLC, UV-Vis, FT-IR, and H-NMR, and purified by semi-preparative HPLC. The pigment was non-toxic to brine shrimp (LD50 > 2.3 g L-1) and was stable at pH 6-10 at temperatures below 60 °C. HPLC analysis shows that the pigment is composed of four major blue fractions. The physicochemical properties and structural analysis demonstrate that this pigment belongs to the indochrome isomers, whose properties have yet to have been characterized. The high solubility in water, good stability in neutral and basic pH, and negligible toxicity of the blue pigment make it a good candidate suitable for several industrial and possibly some food applications.
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Affiliation(s)
- Sebastian Finger
- Facultad de Medicina y Ciencia, Universidad San Sebastián, Lago Panguipulli 1390, 5501842, Puerto Montt, Chile
| | - Félix A Godoy
- Centro i-mar, Universidad de Los Lagos, Camino a Chinquihue s/n km 6, Puerto Montt, Chile.
| | - Geraldine Wittwer
- Centro i-mar, Universidad de Los Lagos, Camino a Chinquihue s/n km 6, Puerto Montt, Chile
| | - Carlos P Aranda
- Departamento de Ciencias Biológicas y Biodiversidad, Universidad de Los Lagos, Av. Fuchslocher 1305, Osorno, Chile
| | - Raúl Calderón
- Centro de Investigación en Recursos Naturales y Sustentabilidad, Universidad Bernardo O'Higgins, Fábrica 1990, Santiago, Chile.,Instituto de Investigaciones Agropecuarias, INIA La Platina, Santa Rosa 11610, Santiago, Chile
| | - Claudio D Miranda
- Laboratorio de Patobiología Acuática, Departamento de Acuicultura, Universidad Católica del Norte, Larrondo 1281, Coquimbo, Chile
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Tuning of the Carbon-to-Nitrogen Ratio for the Production of l-Arginine by Escherichia coli. FERMENTATION-BASEL 2017. [DOI: 10.3390/fermentation3040060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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